Errors caused by R-version conflicts

[jonbra]

Hi,
There seems to be some conflicts with the version of R and some packages, maybe only the package scales. The entire pipeline ran smoothly with the test data, but on my own data this error arose:

Mar-15 14:07:32.450 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'MOSDEPT
H_AMPLICON_PLOT'

Caused by:
  Process `MOSDEPTH_AMPLICON_PLOT` terminated with an error exit status (1)

Command executed:

  plot_mosdepth_regions.r \
      --input_files SWIFT25213950.trim.mkD.amplicon.regions.bed.gz \
      --input_suffix .trim.mkD.amplicon.regions.bed.gz \
      --output_dir ./ \
      --output_suffix .trim.mkD.amplicon.regions

Command exit status:
  1

Command output:
  (empty)

Command error:
  package ‘scales’ was built under R version 3.6.3 
  Loading required package: grid
  ========================================
  ComplexHeatmap version 2.2.0
  Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
  Github page: https://github.com/jokergoo/ComplexHeatmap
  Documentation: http://jokergoo.github.io/ComplexHeatmap-reference
  
  If you use it in published research, please cite:
  Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
    genomic data. Bioinformatics 2016.
  ========================================
  
  Loading required package: viridisLite
  
  Loading required package: viridisLite
  
  Attaching package: ‘viridis’
  
  The following object is masked from ‘package:scales’:
  
      viridis_pal
  
  Warning messages:
  1: package ‘viridis’ was built under R version 3.6.3 
  2: package ‘viridisLite’ was built under R version 3.6.3 
  ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──
  ✔ tibble  3.0.1     ✔ dplyr   1.0.0
  ✔ tidyr   1.1.0     ✔ stringr 1.4.0
  ✔ readr   1.3.1     ✔ forcats 0.5.0
  ✔ purrr   0.3.4     
  ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
  ✖ readr::col_factor() masks scales::col_factor()
  ✖ purrr::discard()    masks scales::discard()
  ✖ dplyr::filter()     masks stats::filter()
  ✖ dplyr::lag()        masks stats::lag()
  Warning messages:
  1: package ‘tidyverse’ was built under R version 3.6.3 
  2: package ‘tibble’ was built under R version 3.6.3 
  3: package ‘tidyr’ was built under R version 3.6.3 
  4: package ‘readr’ was built under R version 3.6.3 
  5: package ‘purrr’ was built under R version 3.6.3 
  6: package ‘dplyr’ was built under R version 3.6.3 
  7: package ‘stringr’ was built under R version 3.6.3 
  8: package ‘forcats’ was built under R version 3.6.3 
  Error:   Dimensions exceed 50 inches (height and width are specified in 'cm' not pixels).
    If you're sure you want a plot that big, use `limitsize = FALSE`.
  Backtrace:
      █
   1. └─ggplot2::ggsave(...)
   2.   └─ggplot2:::plot_dim(...)
  Execution halted

[drpatelh]

Apologies for the late response @jonbra ! Did you manage to get to the bottom of this?

[drpatelh]

We have been threatening to release v2.0 for a while now but hopefully soon 🤞🏽 If you haven't already be great if you can test with

nextflow pull nf-core/viralrecon
nextflow run nf-core/viralrecon ......... -r dev

[drpatelh]

Will close this for now but feel free to re-open if the issue persists in the upcoming release @jonbra 👍🏽